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Toward Crowdsourced Drug Discovery: Start-Up of the Volunteer Computing Project SiDock@home

Part of the Communications in Computer and Information Science book series (CCIS,volume 1510)

Abstract

In this paper, we describe the experience of setting up a computational infrastructure based on BOINC middleware and running a volunteer computing project on its basis. We characterize the first series of computational experiments and review the project’s development in its first six months. The gathered experience shows that BOINC-based Desktop Grids allow to efficiently aid drug discovery at its early stages.

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References

  1. Gerasim@home main page. https://gerasim.boinc.ru/. Accessed 12 May 2021

  2. LHC@home. https://lhcathome.web.cern.ch. Accessed 12 May 2021

  3. Einstein@Home. https://einsteinathome.org. Accessed 12 May 2021

  4. Folding@home - fighting disease with a world wide distributed super computer (2020). https://foldingathome.org. Accessed 12 May 2021

  5. Anderson, D.P.: BOINC: a platform for volunteer computing. J. Grid Comput. 18, 99–122 (2020)

    Google Scholar 

  6. Together We Are Powerful - Folding@home. https://foldingathome.org. Accessed 12 May 2021

  7. Rosetta@home. https://boinc.bakerlab.org. Accessed 12 May 2021

  8. World Community Grid - home. https://www.worldcommunitygrid.org/. Accessed 12 May 2021

  9. TN-Grid. http://gene.disi.unitn.it/test/. Accessed 12 May 2021

  10. IberCIVIS. https://boinc.ibercivis.es/. Accessed 12 May 2021

  11. Ivashko, E., Nikitina, N., Möller, S.: High-performance virtual screening in a BOINC-based enterprise desktop grid. Vestnik Yuzhno-Ural’skogo Gosudarstvennogo Universiteta. Seriya “Vychislitelnaya Matematika i Informatika” 4(1), 57–63 (2015). (in Russian)

    Google Scholar 

  12. Distributed Computing - Computing Platforms. http://distributedcomputing.info/platforms.html. Accessed 12 May 2021

  13. Puertas-Martín, S., et al.: Is high performance computing a requirement for novel drug discovery and how will this impact academic efforts? Expert Opin. Drug Discov. 15(9), 981–985 (2020). PMID: 32345062

    Google Scholar 

  14. Sarvagalla, S., Kondapuram, S.K., Devi, R.V., Coumar, M.S.: Resources for docking-based virtual screening. In: Coumar, M.S. (ed.) Molecular Docking for Computer-Aided Drug Design, pp. 179–203. Academic Press, Cambridge (2021)

    Google Scholar 

  15. Shoichet, B.K., McGovern, S.L., Wei, B., Irwin, J.J.: Lead discovery using molecular docking. Curr. Opin. Chem. Biol. 6(4), 439–446 (2002)

    Google Scholar 

  16. Pagadala, N.S., Syed, K., Tuszynski, J.: Software for molecular docking: a review. Biophys. Rev. 9(2), 91–102 (2017). https://doi.org/10.1007/s12551-016-0247-1

    Google Scholar 

  17. CmDock. https://gitlab.com/Jukic/cmdock. Accessed 12 May 2021

  18. Ruiz-Carmona, S., et al.: rDock: a fast, versatile and open source program for docking ligands to proteins and nucleic acids. PLoS Comput. Biol. 10(4), e1003571 (2014)

    Google Scholar 

  19. Ghare, G.D., Leutenegger, S.T.: Improving speedup and response times by replicating parallel programs on a SNOW. In: Feitelson, D.G., Rudolph, L., Schwiegelshohn, U. (eds.) JSSPP 2004. LNCS, vol. 3277, pp. 264–287. Springer, Heidelberg (2005). https://doi.org/10.1007/11407522_15

    Google Scholar 

  20. CreditNew - BOINC. https://boinc.berkeley.edu/trac/wiki/CreditNew. Accessed 12 May 2021

  21. SiDock@home. https://sidock.si/sidock. Accessed 12 May 2021

  22. Home - COVID.SI. https://covid.si/en. Accessed 12 May 2021

  23. Modeling of the SARS-CoV-2 Genome using I-TASSER. https://zhanglab.ccmb.med.umich.edu/COVID-19. Accessed 12 May 2021

  24. Nikitina, N., Manzyuk, M., Podlipnik, Č., Jukić, M.: Volunteer computing project SiDock@home for virtual drug screening against SARS-CoV-2 (submitted)

    Google Scholar 

  25. Nikitina, N., Manzyuk, M., Podlipnik, Č., Jukić, M.: Performance estimation of a BOINC-based Desktop Grid for large-scale molecular docking (2021, submitted)

    Google Scholar 

  26. WrapperApp - BOINC (2020). https://boinc.berkeley.edu/trac/wiki/WrapperApp. Accessed 12 May 2021

  27. Manzyuk, M., Nikitina, N., Vatutin, E.: Start-Up and the results of the volunteer computing project RakeSearch. In: Voevodin, V., Sobolev, S. (eds.) RuSCDays 2019. CCIS, vol. 1129, pp. 725–734. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-36592-9_59

    Google Scholar 

  28. Cloud Computing Services | Microsoft Azure. https://azure.microsoft.com/en-us/. Accessed 12 May 2021

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Acknowledgements

The first initial library (one billion of compounds) was prepared with the generous help of Microsoft that donated computational resources in the Azure cloud platform [28]. We all from COVID.SI are grateful and looking forward to future collaborations.

We would like to thank all volunteers who provide their computers to the project. Discussions and advice on the project forum are greatly appreciated.

Funding

This work was partly supported by the Scholarship of the President of the Russian Federation for young scientists and graduate students (project “Game-theoretical mathematical models and algorithms for scheduling in high-performance heterogeneous computational systems”), the Slovenian Ministry of Science and Education infrastructure, project grant HPC-RIVR, and by the Slovenian Research Agency (ARRS), programme P2-0046 and J1-2471, the Physical Chemistry programme grant P1-0201; Slovenian Ministry of Education, Science and Sports programme grant OP20.04342.

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Correspondence to Natalia Nikitina .

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Nikitina, N., Manzyuk, M., Jukić, M., Podlipnik, Č., Kurochkin, I., Albertian, A. (2021). Toward Crowdsourced Drug Discovery: Start-Up of the Volunteer Computing Project SiDock@home. In: Voevodin, V., Sobolev, S. (eds) Supercomputing. RuSCDays 2021. Communications in Computer and Information Science, vol 1510. Springer, Cham. https://doi.org/10.1007/978-3-030-92864-3_39

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  • DOI: https://doi.org/10.1007/978-3-030-92864-3_39

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  • Online ISBN: 978-3-030-92864-3

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